Bad machine work or am i over looking something?

Line hone or bore? i can't find my paper work right now so i don't know. It was done with the studs installed. and the deck was squared as well to get my "0" deck, all the way across the deck. The deck was high on left front and on the right side rear. had to be squared as well as decked to get the pistons flush.

So do you thing i need to clearance ALL the caps for studs, or just the thrust, aka #3 cap.

Edit: Found it. Line bore checked and line honed.